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- PDB-1ulr: Crystal structure of tt0497 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1ulr
TitleCrystal structure of tt0497 from Thermus thermophilus HB8
Componentsputative acylphosphatase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity
Similarity search - Function
Acylphosphatase / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsAgo, H. / Hamada, K. / Sugahara, M. / Kuroishi, C. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of tt0497 from Thermus thermophilus HB8
Authors: Ago, H. / Hamada, K. / Sugahara, M. / Kuroishi, C. / Kuramitsu, S. / Yokoyama, S. / Miyano, M.
History
DepositionSep 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative acylphosphatase


Theoretical massNumber of molelcules
Total (without water)9,6941
Polymers9,6941
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.911, 45.727, 49.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein putative acylphosphatase


Mass: 9694.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKS6, acylphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.47 Å3/Da / Density % sol: 15.88 %
Crystal growMethod: micro batch using tera / Details: micro batch using TERA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.09→33.73 Å / Num. obs: 18506 / % possible obs: 63.7 %
Reflection shellResolution: 1.09→1.13 Å / % possible all: 5.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ACY

2acy


Resolution: 1.3→33.71 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.027 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21632 1594 10.1 %RANDOM
Rwork0.18666 ---
obs0.18958 14207 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.975 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.3→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms677 0 0 151 828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021681
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.972917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.303586
X-RAY DIFFRACTIONr_chiral_restr0.1110.299
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02515
X-RAY DIFFRACTIONr_nbd_refined0.2070.2311
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.268
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.232
X-RAY DIFFRACTIONr_mcbond_it0.7961.5428
X-RAY DIFFRACTIONr_mcangle_it1.3262673
X-RAY DIFFRACTIONr_scbond_it2.073253
X-RAY DIFFRACTIONr_scangle_it3.1684.5244
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 115 -
Rwork0.241 989 -
obs-989 100 %

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